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(-) Description

Title :  DOCKING OF THE MODIFIED RF1 X-RAY STRUCTURE INTO THE LOW RESOLUTION CRYO-EM MAP OF E.COLI 70S RIBOSOME BOUND WITH RF1
 
Authors :  U. Rawat, H. Gao, A. Zavialov, R. Gursky, M. Ehrenberg, J. Frank
Date :  31 Jan 06  (Deposition) - 04 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  12.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Rf1 Ribosome Cryo-Em, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Rawat, H. Gao, A. Zavialov, R. Gursky, M. Ehrenberg, J. Frank
Interactions Of The Release Factor Rf1 With The Ribosome As Revealed By Cryo-Em.
J. Mol. Biol. V. 357 1144 2006
PubMed-ID: 16476444  |  Reference-DOI: 10.1016/J.JMB.2006.01.038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRFA
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RF-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2FVO)

(-) Sites  (0, 0)

(no "Site" information available for 2FVO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FVO)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FVO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RF_PROK_IPS00745 Prokaryotic-type class I peptide chain release factors signature.RF1_THEMA204-220  1A:204-220

(-) Exons   (0, 0)

(no "Exon" information available for 2FVO)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:314
 aligned with RF1_THEMA | Q9X183 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
            RF1_THEMA     1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL 333
               SCOP domains d2fvoa1 A:1-333 Peptide chain release factor 1, RF1                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................................................................................................................................................................................................---------....................................................----------....................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RF_PROK_I        ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fvo A   1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG---------ESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQ----------RSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |  -      |220       230       240       250       260       | -       280       290       300       310       320       330   
                                                                                                                                                                                                                                        207       217                                                268        279
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FVO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FVO)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RF1_THEMA | Q9X183)
molecular function
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003747    translation release factor activity    Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RF1_THEMA | Q9X183: 1rq0

(-) Related Entries Specified in the PDB File

1rq0 CRYSTAL STRUCTURE OF PEPTIDE RELEASING FACTOR 1 RELATED ID: EMD-1184 RELATED DB: EMDB RELEASE COMPLEX BOUND WITH RF1 (WT) RELATED ID: EMD-1185 RELATED DB: EMDB RELEASE COMPLEX BOUND WITH RF1 (GAQ)